It is weird why I always receive the digest of the mailing list but the specific topic?
On Tue, Sep 27, 2011 at 9:14 AM, Liu, Liang <[email protected]> wrote: > > Thanks. >> > >> > Is this position restraint same to the one "Position Restrained MD". I >> > see some tutorial shows there are always three step to perform a >> > simulation: Energy minimization, Position Restrained MD and MD >> Simulation. >> >> "Always" is too strong, but this is common. >> >> >> > Is it possible to fulfill the position restraint during Position >> > Restrained MD? Thanks. >> >> Yes, hence the name. How well they can be fulfilled depends on the >> initial and simulation conditions. >> > > Thanks for this information. > But how to perform a harmonic potential to all the heavy atoms of RNA? > Justin said this one should be adjusted in the posre.itp file, and what I > see in the file is all 1000. Does this means k=1000 in the equation of E = k > (r-r0)^2? > Thanks. > > >> >> Mark >> > > -- > Best, > Liang Liu > -- Best, Liang Liu
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